I am eager to change the pickups in my strat and am torn between these 2 choices. Plenty of fans of the 69s on here I am assuming. But Ive heard some clips of the Van Zandts and they sound really good as well, this clip in particular (granted that is a marvelous amp in its own right. Can they 69s do tones like this as well as the Jerry thing?

I don't know about the Van Zandt pickups. But the D. Allen 69's and a Strat-O-Blaster are going to get you all of the Jerryness you are going to get out of a Strat. Why try to deviate from a proven formula?